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protocols::noesy_assign Namespace Reference

Classes

class  CovalentCompliance
 
class  CrossPeak
 
class  CrossPeak3D
 
class  CrossPeak4D
 
class  CrossPeakInfo
 shared information about CrossPeak (one for each proton dimension) More...
 
class  CrossPeakList
 
class  NoesyModule
 
class  DistanceScoreMover
 maintains a list of constraints_ (each PeakAssignment yields one) and peak_constraints_ ( each cross peak with multiple assignments creates one AmbiguousNMRConstraint ). the DistanceMover (prepare scoring and apply directly interacts with the Dk term in CrossPeak (set_decoy_compatibility) More...
 
class  EXCN_NoesyAssign
 
class  EXCN_UnknownAtomname
 
class  EXCN_UnknownResonance
 
class  EXCN_AssignmentNotFound
 
class  EXCN_FileFormat
 
class  FloatingResonance
 
class  FoldResonance
 
class  FragsToAtomDist
 
class  MethylNames
 
class  MethylNameLibrary
 
class  PeakAssignment
 fast access to assignments that are stored in CrossPeak – similar to FragID More...
 
class  PeakAssignmentParameters
 
class  PeakAssignmentResidueMap
 fast access to assignments by residue number More...
 
class  PeakCalibrator
 
class  PeakCalibratorMap
 
class  PeakFileFormat_Base
 
class  PeakFileFormat
 
class  PeakFileFormat_xeasy
 
class  PeakFileFormat_Sparky
 
class  PeakFileFormat_xpk
 
class  Resonance
 
class  ResonanceList
 
class  StructureDependentPeakCalibrator
 
class  StructureIndependentPeakCalibrator
 

Typedefs

typedef
utility::pointer::owning_ptr
< PeakAssignment
PeakAssignmentOP
 
typedef
utility::pointer::owning_ptr
< PeakAssignment const > 
PeakAssignmentCOP
 
typedef
utility::pointer::access_ptr
< PeakAssignment
PeakAssignmentAP
 
typedef
utility::pointer::access_ptr
< PeakAssignment const > 
PeakAssignmentCAP
 
typedef
utility::pointer::owning_ptr
< CrossPeak
CrossPeakOP
 
typedef
utility::pointer::owning_ptr
< CrossPeak const > 
CrossPeakCOP
 
typedef
utility::pointer::access_ptr
< CrossPeak
CrossPeakAP
 
typedef
utility::pointer::access_ptr
< CrossPeak const > 
CrossPeakCAP
 
typedef
utility::pointer::owning_ptr
< CrossPeakInfo
CrossPeakInfoOP
 
typedef
utility::pointer::owning_ptr
< CrossPeakInfo const > 
CrossPeakInfoCOP
 
typedef
utility::pointer::access_ptr
< CrossPeakInfo
CrossPeakInfoAP
 
typedef
utility::pointer::access_ptr
< CrossPeakInfo const > 
CrossPeakInfoCAP
 
typedef
utility::pointer::owning_ptr
< CrossPeakList
CrossPeakListOP
 
typedef
utility::pointer::owning_ptr
< CrossPeakList const > 
CrossPeakListCOP
 
typedef
utility::pointer::access_ptr
< CrossPeakList
CrossPeakListAP
 
typedef
utility::pointer::access_ptr
< CrossPeakList const > 
CrossPeakListCAP
 
typedef
utility::pointer::owning_ptr
< DistanceScoreMover
DistanceScoreMoverOP
 
typedef
utility::pointer::owning_ptr
< DistanceScoreMover const > 
DistanceScoreMoverCOP
 
typedef
utility::pointer::access_ptr
< DistanceScoreMover
DistanceScoreMoverAP
 
typedef
utility::pointer::access_ptr
< DistanceScoreMover const > 
DistanceScoreMoverCAP
 
typedef
utility::pointer::owning_ptr
< FloatingResonance
FloatingResonanceOP
 
typedef
utility::pointer::owning_ptr
< FloatingResonance const > 
FloatingResonanceCOP
 
typedef
utility::pointer::access_ptr
< FloatingResonance
FloatingResonanceAP
 
typedef
utility::pointer::access_ptr
< FloatingResonance const > 
FloatingResonanceCAP
 
typedef utility::vector1
< core::Size
SizeList
 
typedef utility::vector1
< std::pair< std::string,
SizeList > > 
AtomGrps
 
typedef utility::vector1
< AtomGrps
GroupList
 
typedef std::map
< core::id::AtomID,
FragsToAtomDist::DistanceRecord
InnerMap
 
typedef std::map
< core::id::AtomID, InnerMap
DistanceMap
 
typedef
utility::pointer::owning_ptr
< FragsToAtomDist
FragsToAtomDistOP
 
typedef
utility::pointer::owning_ptr
< FragsToAtomDist const > 
FragsToAtomDistCOP
 
typedef
utility::pointer::access_ptr
< FragsToAtomDist
FragsToAtomDistAP
 
typedef
utility::pointer::access_ptr
< FragsToAtomDist const > 
FragsToAtomDistCAP
 
typedef
utility::pointer::owning_ptr
< NoesyModule
NoesyModuleOP
 
typedef
utility::pointer::owning_ptr
< NoesyModule const > 
NoesyModuleCOP
 
typedef
utility::pointer::access_ptr
< NoesyModule
NoesyModuleAP
 
typedef
utility::pointer::access_ptr
< NoesyModule const > 
NoesyModuleCAP
 
typedef
PeakAssignmentResidueMap::PeakAssignments 
PeakAssignments
 
typedef
utility::pointer::owning_ptr
< PeakAssignmentResidueMap
PeakAssignmentResidueMapOP
 
typedef
utility::pointer::owning_ptr
< PeakAssignmentResidueMap
const > 
PeakAssignmentResidueMapCOP
 
typedef
utility::pointer::access_ptr
< PeakAssignmentResidueMap
PeakAssignmentResidueMapAP
 
typedef
utility::pointer::access_ptr
< PeakAssignmentResidueMap
const > 
PeakAssignmentResidueMapCAP
 
typedef std::bitset< MAX_TYPECalibrationTypeCumulator
 
typedef
utility::pointer::owning_ptr
< PeakCalibrator
PeakCalibratorOP
 
typedef
utility::pointer::owning_ptr
< PeakCalibrator const > 
PeakCalibratorCOP
 
typedef
utility::pointer::access_ptr
< PeakCalibrator
PeakCalibratorAP
 
typedef
utility::pointer::access_ptr
< PeakCalibrator const > 
PeakCalibratorCAP
 
typedef
utility::pointer::owning_ptr
< PeakFileFormat
PeakFileFormatOP
 
typedef
utility::pointer::owning_ptr
< PeakFileFormat const > 
PeakFileFormatCOP
 
typedef
utility::pointer::owning_ptr
< Resonance
ResonanceOP
 
typedef
utility::pointer::owning_ptr
< Resonance const > 
ResonanceCOP
 
typedef
utility::pointer::access_ptr
< Resonance
ResonanceAP
 
typedef
utility::pointer::access_ptr
< Resonance const > 
ResonanceCAP
 
typedef
utility::pointer::owning_ptr
< ResonanceList
ResonanceListOP
 
typedef
utility::pointer::owning_ptr
< ResonanceList const > 
ResonanceListCOP
 
typedef
utility::pointer::access_ptr
< ResonanceList
ResonanceListAP
 
typedef
utility::pointer::access_ptr
< ResonanceList const > 
ResonanceListCAP
 

Enumerations

enum  CALIBRATION_ATOM_TYPE {
  BACKBONE = 1, BETA_NON_METHYL, METHYL, SIDECHAIN,
  MAX_TYPE
}
 

Functions

bool fall_back (core::id::NamedAtomID const &_atom1, core::id::NamedAtomID const &_atom2)
 
core::Real round (core::Real d, core::Size digits)
 
Real sigmoid (Real x, Real tau, Real m, int sign=1)
 
std::ostream & operator<< (std::ostream &os, CrossPeak const &peak)
 
std::ostream & operator<< (std::ostream &os, CrossPeakInfo const &cpi)
 
void open_stream (utility::io::ozstream &os, std::string const &prefix, std::string const &peak_filename)
 
std::ostream & operator<< (std::ostream &os, FragsToAtomDist::DistanceRecord const &dr)
 
std::istream & operator>> (std::istream &is, FragsToAtomDist::DistanceRecord &dr)
 
void initialize_group_list (GroupList &grp_list, core::pose::Pose const &pose)
 
void store_distmap_with_namedatoms (FragsToAtomDist::NamedDistanceMap &named_distmap, DistanceMap const &distmap, GroupList const &proton_groups)
 
void store_distance_snapshot (DistanceMap &distmap, core::pose::Pose const &short_pose, Size start, Size short_size, GroupList const &grps)
 
std::istream & operator>> (std::istream &, FragsToAtomDist::DistanceRecord const &)
 
std::ostream & operator<< (std::ostream &os, PeakAssignment const &pa)
 
void retrieve_assignment (PeakAssignments const &list, Size resonance_id1, Size resonance_id2, PeakAssignments &intra_res_NOEs)
 
Real sum_IntraNOE (PeakAssignments const &list, id::NamedAtomID const &atom1, id::NamedAtomID const &atom2)
 
Real sum_peak_volumes (PeakAssignments const &list, core::Size i, core::Size j)
 
Size const TOL_H_INDIRECT (1)
 
Size const TOL_H_DIRECT (2)
 
Size const TOL_LABEL (3)
 
void process_last_resonances (std::deque< ResonanceOP > &last_resonances, bool drain=false)
 
bool covalent_compliance (core::id::NamedAtomID const &atom1, core::id::NamedAtomID const &atom2)
 

Variables

PeakAssignment const BOGUS_ASSIGNMENT (NULL, 0, 0)
 

Typedef Documentation

typedef utility::vector1< std::pair< std::string, SizeList> > protocols::noesy_assign::AtomGrps

Enumeration Type Documentation

Enumerator
BACKBONE 
BETA_NON_METHYL 
METHYL 
SIDECHAIN 
MAX_TYPE 

Function Documentation

bool protocols::noesy_assign::covalent_compliance ( core::id::NamedAtomID const &  atom1,
core::id::NamedAtomID const &  atom2 
)
bool protocols::noesy_assign::fall_back ( core::id::NamedAtomID const &  _atom1,
core::id::NamedAtomID const &  _atom2 
)
void protocols::noesy_assign::initialize_group_list ( GroupList &  grp_list,
core::pose::Pose const &  pose 
)
void protocols::noesy_assign::open_stream ( utility::io::ozstream &  os,
std::string const &  prefix,
std::string const &  peak_filename 
)
std::ostream & protocols::noesy_assign::operator<< ( std::ostream &  os,
CrossPeakInfo const &  cpi 
)
std::ostream & protocols::noesy_assign::operator<< ( std::ostream &  os,
FragsToAtomDist::DistanceRecord const &  dr 
)
std::ostream & protocols::noesy_assign::operator<< ( std::ostream &  os,
PeakAssignment const &  pa 
)
std::ostream& protocols::noesy_assign::operator<< ( std::ostream &  os,
CrossPeak const &  peak 
)
inline
std::istream& protocols::noesy_assign::operator>> ( std::istream &  is,
FragsToAtomDist::DistanceRecord &  dr 
)
std::istream& protocols::noesy_assign::operator>> ( std::istream &  ,
FragsToAtomDist::DistanceRecord const &   
)
void protocols::noesy_assign::process_last_resonances ( std::deque< ResonanceOP > &  last_resonances,
bool  drain = false 
)
void protocols::noesy_assign::retrieve_assignment ( PeakAssignments const &  list,
Size  resonance_id1,
Size  resonance_id2,
PeakAssignments &  intra_res_NOEs 
)
core::Real protocols::noesy_assign::round ( core::Real  d,
core::Size  digits 
)
Real protocols::noesy_assign::sigmoid ( Real  x,
Real  tau,
Real  m,
int  sign = 1 
)
void protocols::noesy_assign::store_distance_snapshot ( DistanceMap &  distmap,
core::pose::Pose const &  short_pose,
Size  start,
Size  short_size,
GroupList const &  grps 
)
void protocols::noesy_assign::store_distmap_with_namedatoms ( FragsToAtomDist::NamedDistanceMap &  named_distmap,
DistanceMap const &  distmap,
GroupList const &  proton_groups 
)
Real protocols::noesy_assign::sum_IntraNOE ( PeakAssignments const &  list,
id::NamedAtomID const &  atom1,
id::NamedAtomID const &  atom2 
)
Real protocols::noesy_assign::sum_peak_volumes ( PeakAssignments const &  list,
core::Size  i,
core::Size  j 
)
Size const protocols::noesy_assign::TOL_H_DIRECT ( )
Size const protocols::noesy_assign::TOL_H_INDIRECT ( )
Size const protocols::noesy_assign::TOL_LABEL ( )

Variable Documentation

PeakAssignment const protocols::noesy_assign::BOGUS_ASSIGNMENT